Both Positive and Negative Selection Pressures Contribute to the Polymorphism Pattern of the Duplicated Human CYP21A2 Gene.

The human steroid 21-hydroxylase gene (CYP21A2) participates in cortisol and aldosterone biosynthesis, and resides together with its paralogous (duplicated) pseudogene in a multiallelic copy number variation (CNV), called RCCX CNV. Concerted evolution caused by non-allelic gene conversion has been described in great ape CYP21 genes, and the same conversion activity is responsible for a serious genetic disorder of CYP21A2, congenital adrenal hyperplasia (CAH). In the current study, 33 CYP21A2 haplotype variants encoding 6 protein variants were determined from a European population. CYP21A2 was shown to be one of the most diverse human genes (HHe=0.949), but the diversity of intron 2 was greater still. Contrary to previous findings, the evolution of intron 2 did not follow concerted evolution, although the remaining part of the gene did. Fixed sites (different fixed alleles of sites in human CYP21 paralogues) significantly accumulated in intron 2, indicating that the excess of fixed sites was connected to the lack of effective non-allelic conversion and concerted evolution. Furthermore, positive selection was presumably focused on intron 2, and possibly associated with the previous genetic features. However, the positive selection detected by several neutrality tests was discerned along the whole gene. In addition, the clear signature of negative selection was observed in the coding sequence. The maintenance of the CYP21 enzyme function is critical, and could lead to negative selection, whereas the presumed gene regulation altering steroid hormone levels via intron 2 might help fast adaptation, which broadly characterizes the genes of human CNVs responding to the environment

Scale representation of the segregating sites of human <i>CYP21</i> genes.

<p>Boxes symbolize the exons, red indicates the coding region, pink shows the untranslated regions. Segregating sites are denoted by their position, numbered from the start of the <i>CYP21A2</i> coding region in the sequence NT_007592.15: 31945792-31949720. The segregating site of the <i>CYP21A2</i> gene can be seen above the depicted gene. The segregating site of the <i>CYP21A1P</i> gene derived from an external dataset can be found below the depicted gene.</p

Rooted maximum likelihood phylogenetic trees constructed from selected full-length sequences, intron 2 sequences and <i>CYP21</i> gene sequences without intron 2 of the great ape <i>CYP21</i> sequence dataset.

<p>The names of <i>CYP21</i> sequences of HLA-homozygous cell lines available from public databases are represented at the human sequences. Bootstrap values are shown next to the corresponding nodes, but the values within human clades are not presented for clarity. The scale bar indicates genetic distance. (A) Rooted ML tree of great ape <i>CYP21</i> full-length gene. (B) Rooted ML tree of great ape <i>CYP21</i> intron 2. (C) Rooted ML tree of great ape <i>CYP21</i> genes without intron 2.</p

Scaled representation of the organization of human RCCX copy number variation (CNV) depicted by mono-, bi- and trimodular RCCX structure variants.

<p>The schematic abbreviations of RCCX structures are indicated on the left side; a module (a repeat) is abbreviated with two letters, the first represents the alleles of HERV-K CNV (L – the long allele or S – short allele [The abbreviation of these alleles comes from the traditional usage of long and short <i>C4</i> genes.]), and the second symbolizes the types of <i>C4</i> gene (A or B). The duplication of these two letters indicates bimodular RCCX structure, while the triplicate of the two letters means trimodular RCCX structures. Dotted lines indicate the module boundaries, and the directions of the ends of chromosome 6 are indicated by arrows under the scale bar. The variable region of bimodular RCCX contains two pairs of full-length genes, complement component 4 (<i>C4A</i> and <i>C4B</i>), steroid 21-hydroxylase (<i>CYP21A1P</i> and <i>CYP21A2</i>), and two pairs of a functional gene and a truncated pseudogene, serine/threonine kinase 19 (<i>STK19</i> and <i>STK19P</i>) and tenascin-X (<i>TNXA</i> and <i>TNXB</i>). The illustrated region spans from the telomeric end of exon 4 of <i>STK19</i> to the centromeric end of exon 28 of <i>TNXB</i>.</p

Spatial distributions of phylogenetic signals derived from the different orthologous and paralogous pairs of the human and chimpanzee full-length <i>CYP21</i> sequences.

<p>Blue line indicates the phlyogenetic signal of human paralogues (hA2-hA1P), red dashed line indicates <i>CYP21A2</i> orthologues (hA2-cA2), orange line indicates chimpanzee paralogues (cA2-cA1P) and green dashed line indicates <i>CYP21A1P</i> orthologues (hA1P-cA1P). The likelihood of closely related sequences to resemble each other more than random sequences of the same phylogenetic tree is expressed by ‘% of permutated trees’ in y axis. Schematic <i>CYP21</i> genes are indicated below the plot, high white boxes symbolize the exons, low white boxes represent the untranslated regions, and black lines indicate the introns and flanking regions.</p